Re: [gmx-users] Gromacs installation with GPU support in Windows 7

2018-05-29 Thread Jia Hong 
My bad, I missed a line in the warning message:

Building NVCC (Device) object 
src/gromac/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/Release/libgromacs_generated_nbnxn_cuda.cu.obj

   CMake Warning (dev) at 
libgromacs_generated_nbnxn_cuda.cu.obj.Release.cmake:74:
   Syntax Warning in cmake code at column 28


   Argument not separated from preceding token by whitespace.
 This warning is for project developers. Use -Wno-dev to suppress it.






From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Jia Hong 

Sent: Wednesday, May 30, 2018 9:28 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Gromacs installation with GPU support in Windows 7

Hi,


I've implemented the fix and I verified that it works on the command line; I've 
successfully complied the nvcc depend file.

Nonetheless, CMake still fails on compiling in that stage. Here is the error 
message in Visual studio 2015

CMake Error at libgromacs_generated_nbnxn_cuda.cu.obj.Release.cmake:223 
(message):
 Error generating
 
C:/tools/GROMACS/gromacs-2018.1/build_gpu/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/Release/libgromacs_generated_nbnxn_cuda.cu.obj


If this is of any use, there's also an accompanying warning message appearing 
right before the error message I showed above:

Building NVCC (Device) object 
src/gromac/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/Release/libgromacs_generated_nbnxn_cuda.cu.obj
   Syntax Warning in cmake code at column 28
   Argument not separated from preceding token by whitespace.
 This warning is for project developers. Use -Wno-dev to suppress it.

The system specs I'm using:

  *   Windows 7
  *   VS 2015
 *   VS 2015 developer prompt to manually compile the file CMake was trying 
to compile
  *   CMake 3.11 GUI
  *   CUDA v9.1 - I've verified my CUDA installation with the provided build 
examples.
  *   Graphics card: GTX 1080


I do not know if CMake deals with whitespace paths, but when compiling 
manually, I had to make sure to add quotes around my cuda path and my --ccbin 
path because they are installed in directories with whitespaces.

Any help would be greatly appreciated.

Regards,
Harry





From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Aleksei 
Iupinov 
Sent: Tuesday, May 22, 2018 4:59 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Gromacs installation with GPU support in Windows 7

Hello Harry,

Thank you for the report. It seems to be a trivial error in the code,
indeed.
It was not caught by the Gromacs automated testing since we don't have
Windows + CUDA configuration in it.
I have filed a bug report https://redmine.gromacs.org/issues/2509 and this
Bug #2509: Gromacs 2018 does not compile on Windows with CUDA - GROMACS - 
GROMACS development<https://redmine.gromacs.org/issues/2509>
redmine.gromacs.org
Redmine



Bug #2509: Gromacs 2018 does not compile on Windows with CUDA - GROMACS - 
GROMACS development<https://redmine.gromacs.org/issues/2509>
redmine.gromacs.org
Redmine



will be fixed in Gromacs 2018.2.
Meanwhile you can easily fix it yourself.
The line 646 of your src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu looks like
stat = cudaStreamQuery(stream);
and you only have to remove the unused (and undeclared) "stat = " variable,
turning the line into:
cudaStreamQuery(stream);
Please don't hesitate to report if there are any more errors :-)

Cheers,
Aleksei

On Tue, May 22, 2018 at 3:26 AM, Jia Hong  wrote:

> Aim: Install Gromacs with GPU support in windows 7
>
>
> Problem: Build step failed in Visual Studio 14 2015, using CMake 3.11 GUI
> in Windows
>
>
> Identified "issues":
>
>   1.  First off, NVIDIA named their default CUDA installation directory in
> a space separated directory. This caused much grief when CMake complains
> that "Check for working NVCC/C compiler combination - broken" and "CUDA
> compiler does not seem to be functional".
>  *   The solution was to surround the path with quotes in
> CUDA_TOOLKIT_ROOT_DIR
>   2.  Visual Studio fails to compile libgromacs (VS complains that it
> could not find ../../lib/gromacs.lib
>
>
> With regards to (2.), CMake completed the generation of VS build files
> without errors and I tried building it using VS 14 2015 (as specified in my
> CMake generation tool). The steps I took:
>
>   1.  set the build type to Release
>   2.  click build all
>
>
> I also tried compiling Gromacs with the exact same steps, but without GPU
> support, and it went without a hitch.
>
>
> I therefore suspect that it might be that "path issue" I faced earlier
> (1.), so I tried identifying the first error in VS build and it lead me to
> src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu.
>
>
> I copied the commands as-is within the makefile and tried t

Re: [gmx-users] Gromacs installation with GPU support in Windows 7

2018-05-29 Thread Jia Hong 
Hi,


I've implemented the fix and I verified that it works on the command line; I've 
successfully complied the nvcc depend file.

Nonetheless, CMake still fails on compiling in that stage. Here is the error 
message in Visual studio 2015

CMake Error at libgromacs_generated_nbnxn_cuda.cu.obj.Release.cmake:223 
(message):
 Error generating
 
C:/tools/GROMACS/gromacs-2018.1/build_gpu/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/Release/libgromacs_generated_nbnxn_cuda.cu.obj


If this is of any use, there's also an accompanying warning message appearing 
right before the error message I showed above:

Building NVCC (Device) object 
src/gromac/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/Release/libgromacs_generated_nbnxn_cuda.cu.obj
   Syntax Warning in cmake code at column 28
   Argument not separated from preceding token by whitespace.
 This warning is for project developers. Use -Wno-dev to suppress it.

The system specs I'm using:

  *   Windows 7
  *   VS 2015
 *   VS 2015 developer prompt to manually compile the file CMake was trying 
to compile
  *   CMake 3.11 GUI
  *   CUDA v9.1 - I've verified my CUDA installation with the provided build 
examples.
  *   Graphics card: GTX 1080


I do not know if CMake deals with whitespace paths, but when compiling 
manually, I had to make sure to add quotes around my cuda path and my --ccbin 
path because they are installed in directories with whitespaces.

Any help would be greatly appreciated.

Regards,
Harry





From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Aleksei 
Iupinov 
Sent: Tuesday, May 22, 2018 4:59 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Gromacs installation with GPU support in Windows 7

Hello Harry,

Thank you for the report. It seems to be a trivial error in the code,
indeed.
It was not caught by the Gromacs automated testing since we don't have
Windows + CUDA configuration in it.
I have filed a bug report https://redmine.gromacs.org/issues/2509 and this
Bug #2509: Gromacs 2018 does not compile on Windows with CUDA - GROMACS - 
GROMACS development<https://redmine.gromacs.org/issues/2509>
redmine.gromacs.org
Redmine



will be fixed in Gromacs 2018.2.
Meanwhile you can easily fix it yourself.
The line 646 of your src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu looks like
stat = cudaStreamQuery(stream);
and you only have to remove the unused (and undeclared) "stat = " variable,
turning the line into:
cudaStreamQuery(stream);
Please don't hesitate to report if there are any more errors :-)

Cheers,
Aleksei

On Tue, May 22, 2018 at 3:26 AM, Jia Hong  wrote:

> Aim: Install Gromacs with GPU support in windows 7
>
>
> Problem: Build step failed in Visual Studio 14 2015, using CMake 3.11 GUI
> in Windows
>
>
> Identified "issues":
>
>   1.  First off, NVIDIA named their default CUDA installation directory in
> a space separated directory. This caused much grief when CMake complains
> that "Check for working NVCC/C compiler combination - broken" and "CUDA
> compiler does not seem to be functional".
>  *   The solution was to surround the path with quotes in
> CUDA_TOOLKIT_ROOT_DIR
>   2.  Visual Studio fails to compile libgromacs (VS complains that it
> could not find ../../lib/gromacs.lib
>
>
> With regards to (2.), CMake completed the generation of VS build files
> without errors and I tried building it using VS 14 2015 (as specified in my
> CMake generation tool). The steps I took:
>
>   1.  set the build type to Release
>   2.  click build all
>
>
> I also tried compiling Gromacs with the exact same steps, but without GPU
> support, and it went without a hitch.
>
>
> I therefore suspect that it might be that "path issue" I faced earlier
> (1.), so I tried identifying the first error in VS build and it lead me to
> src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu.
>
>
> I copied the commands as-is within the makefile and tried to compile it in
> VS developer command prompt myself.
>
>
> The error I got was:
>
> C:/tools/GROMACS/gromacs-2018.1/src/gromacs/mdlib/nbnxn_cuda/nvnxn_cuda.cu(646):
> error: expression must be a modifiable lvalue.
>
>
>
> My suspicion is that:
>
>   1.  The error "might" be because of a path problem ? (like before)
>   2.  nvnxn_cuda.cu at line 646 has a syntax error. (maybe)
>
>
> Any help would be greatly appreciated.
>
>
> Regards,
>
> Harry.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_g

Re: [gmx-users] Gromacs installation with GPU support in Windows 7

2018-05-22 Thread Aleksei Iupinov 
Hello Harry,

Thank you for the report. It seems to be a trivial error in the code,
indeed.
It was not caught by the Gromacs automated testing since we don't have
Windows + CUDA configuration in it.
I have filed a bug report https://redmine.gromacs.org/issues/2509 and this
will be fixed in Gromacs 2018.2.
Meanwhile you can easily fix it yourself.
The line 646 of your src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu looks like
stat = cudaStreamQuery(stream);
and you only have to remove the unused (and undeclared) "stat = " variable,
turning the line into:
cudaStreamQuery(stream);
Please don't hesitate to report if there are any more errors :-)

Cheers,
Aleksei

On Tue, May 22, 2018 at 3:26 AM, Jia Hong  wrote:

> Aim: Install Gromacs with GPU support in windows 7
>
>
> Problem: Build step failed in Visual Studio 14 2015, using CMake 3.11 GUI
> in Windows
>
>
> Identified "issues":
>
>   1.  First off, NVIDIA named their default CUDA installation directory in
> a space separated directory. This caused much grief when CMake complains
> that "Check for working NVCC/C compiler combination - broken" and "CUDA
> compiler does not seem to be functional".
>  *   The solution was to surround the path with quotes in
> CUDA_TOOLKIT_ROOT_DIR
>   2.  Visual Studio fails to compile libgromacs (VS complains that it
> could not find ../../lib/gromacs.lib
>
>
> With regards to (2.), CMake completed the generation of VS build files
> without errors and I tried building it using VS 14 2015 (as specified in my
> CMake generation tool). The steps I took:
>
>   1.  set the build type to Release
>   2.  click build all
>
>
> I also tried compiling Gromacs with the exact same steps, but without GPU
> support, and it went without a hitch.
>
>
> I therefore suspect that it might be that "path issue" I faced earlier
> (1.), so I tried identifying the first error in VS build and it lead me to
> src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu.
>
>
> I copied the commands as-is within the makefile and tried to compile it in
> VS developer command prompt myself.
>
>
> The error I got was:
>
> C:/tools/GROMACS/gromacs-2018.1/src/gromacs/mdlib/nbnxn_cuda/nvnxn_cuda.cu(646):
> error: expression must be a modifiable lvalue.
>
>
>
> My suspicion is that:
>
>   1.  The error "might" be because of a path problem ? (like before)
>   2.  nvnxn_cuda.cu at line 646 has a syntax error. (maybe)
>
>
> Any help would be greatly appreciated.
>
>
> Regards,
>
> Harry.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Gromacs installation on GPU

2017-03-15 Thread Mark Abraham 
Hi,

The more simple way to cater for all possibilities is to configure with GPU
support the first time. mdrun observes whether there are actually GPUs at
run time and executes accordingly. But as Justin says, this requires that
you install CUDA when you might not use it, which is usually more
inconvenient than a second GROMACS install when you later decide you need
GPU support.

Mark

On Wed, Mar 15, 2017 at 1:55 PM Justin Lemkul  wrote:

>
>
> On 3/15/17 8:43 AM, Andrew Bostick wrote:
> > Dear Gromacs users,
> >
> > I had installed gromacs using following commands:
> >
> > tar xvf cmake-3.6.1.tar.gz
> > tar xvzf gromacs-5.1.3.tar.gz
> >
> > cd ../cmake-3.6.1.
> > ./configure
> > make
> > make install
> >
> > cd ../gromacs-5.1.3
> > mkdir build
> > cd build
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> > -DGMX_MPI=ON -DGMX_GPU=OFF
> > make
> > make check
> > make install
> > source /usr/local/gromacs/bin/GMXRC
> >
> > -
> >
> > Now I want to do MD simulation on GPU.
> >
> > Should I do installation again? Isn't there a more simple way?
> >
>
> The install process requires information about the GPU compatibility of the
> hardware, libraries etc, so yes, if you used -DGMX_GPU=OFF then you need to
> install again (ideally with a current version of GROMACS, or at minimum the
> latest patch release in the 5.1 series, rather than an old version of the
> code).
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Gromacs installation on GPU

2017-03-15 Thread Justin Lemkul 



On 3/15/17 8:43 AM, Andrew Bostick wrote:

Dear Gromacs users,

I had installed gromacs using following commands:

tar xvf cmake-3.6.1.tar.gz
tar xvzf gromacs-5.1.3.tar.gz

cd ../cmake-3.6.1.
./configure
make
make install

cd ../gromacs-5.1.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-DGMX_MPI=ON -DGMX_GPU=OFF
make
make check
make install
source /usr/local/gromacs/bin/GMXRC

-

Now I want to do MD simulation on GPU.

Should I do installation again? Isn't there a more simple way?



The install process requires information about the GPU compatibility of the 
hardware, libraries etc, so yes, if you used -DGMX_GPU=OFF then you need to 
install again (ideally with a current version of GROMACS, or at minimum the 
latest patch release in the 5.1 series, rather than an old version of the code).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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Re: [gmx-users] Gromacs installation on GPU

2016-08-10 Thread Szilárd Páll 
http://manual.gromacs.org/documentation/2016/install-guide/index.html#cuda-gpu-acceleration
--
Szilárd


On Wed, Aug 10, 2016 at 11:47 AM, Atila Petrosian
 wrote:
> *Dear* *Szilárd,  *
>
> *Thanks for your answer,*
>
>> There's the issue. You need to tell the build
>
>> system where CUDA is, e.g. by setting the
>
>> CUDA_TOOLKIT_ROOT_DIR environment variable.
>
> *How? Which command is required in linux?*
>
> *Best, *
>
> *Atila*
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
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Re: [gmx-users] Gromacs installation on GPU

2016-08-09 Thread Szilárd Páll 
On Tue, Aug 9, 2016 at 2:06 PM, Atila Petrosian
 wrote:
> Dear gromacs users,
>
> I am installing gromacs in my system. My computational system is Rocks
> 6.1.1.
>
>  I encountered with following:
>
> [root@me build]# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_GPU=ON
>
> -- The C compiler identification is GNU 4.4.7
> -- The CXX compiler identification is GNU 4.4.7
> -- Check for working C compiler: /usr/bin/cc
> -- Check for working C compiler: /usr/bin/cc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Looking for NVIDIA GPUs present in the system
> -- Number of NVIDIA GPUs detected: 1
> CUDA_TOOLKIT_ROOT_DIR not found or specified
> -- Could NOT find CUDA (missing:  CUDA_TOOLKIT_ROOT_DIR
> CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at
> least version "4.0")

^^^
There's the issue. You need to tell the build system where CUDA is,
e.g. by setting the CUDA_TOOLKIT_ROOT_DIR environment variable.

--
Szilárd

> CMake Error at cmake/gmxManageGPU.cmake:153 (message):
>   mdrun supports native GPU acceleration on NVIDIA hardware with compute
>   capability >= 2.0 (Fermi or later).  This requires the NVIDIA CUDA
> toolkit,
>   which was not found.  Its location can be hinted by setting the
>   CUDA_TOOLKIT_ROOT_DIR CMake option (does not work as an environment
>   variable).  The typical location would be /usr/local/cuda[-version].  Note
>   that CPU or GPU acceleration can be selected at runtime.
>
>   1 NVIDIA GPU(s) found in the system:
>
>   GeForce GTX 480
>
>   Compute capability information not available, consult the NVIDIA website:
>
>   https://developer.nvidia.com/cuda-gpus
> Call Stack (most recent call first):
>   CMakeLists.txt:185 (include)
>
> -- Configuring incomplete, errors occurred!
> See also "/home/host/nasb/gromacs-5.1.1/build/CMakeFiles/CMakeOutput.log".
>
> I am beginner in the installation of gromacs as parallel and on GPU.
>
> Please guide me to solve this problem.
>
> Best,
> Atila
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
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Re: [gmx-users] Gromacs installation on GPU

2016-08-09 Thread Nikhil Maroli 
Dear Atila,
You need to install CUDA toolkit to access the GPU facility .you can get it
from here https://developer.nvidia.com/cuda-toolkit

GeForce GTX 480

Is an old card,i dont know how much you can achieve using this .
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